We use ModernBill for one of our brands, clientexec for another, and lpanel on another.

We don't actively use WHM Autopilot (we have it on a test box), but we have many resellers who do...

Out of all of them, I think ModernBill "wins".. although it is the most complex. Clientexec is easiest for the end-user/customer, and lpanel is.... well.... really not something we like very much. (Doesn't allow multiple domains under one billing account, and their support is horrible.)

AutoPilot (v2) is pretty good. Nice and simple. I'm a bit disappointed with the latest release (v3), bit I suspect that over the next 6 months or so it will slowly get better as the company behind it sorts itself out and eventually publishes some documentation for their API and lets 3rd party developers add functionality that is needed. (like a domain registration/mgmt module)

I'm pretty confident that modernbill will stay as the "leader" in the pack, with their v5 release. The company is well established, has a solid business plan, and the roadmap they have publicly laid out is excellent. I also think that Michael's active participation in the MB forum community is a harbinger of good things. It's evident they are sincerely trying to make things better, and listen to their customers. We'll see.

Ubersmith is one billing system that I haven't actually used in real life.. but their system looks VERY nice. A bit on the spendy side, but well worth it if it makes the user-experience a "non-issue", and is easy for our billing staff to use. We're waiting for their current version to come out of beta, and then we'll be giving that a test.